Assing kernelMatrix class to matrix objects

Description

as.kernelMatrix in package KERE can be used to coerce the kernelMatrix class to matrix objects representing a kernel matrix. These matrices can then be used with the kernelMatrix interfaces which most of the functions in KERE support.

Usage

## S4 method for signature 'matrix'
as.kernelMatrix(x, center = FALSE)

Arguments

Author(s)

Alexandros Karatzoglou
alexandros.karatzoglou@ci.tuwien.ac.at

See Also

kernelMatrix, dots

Examples

## Create toy data
x <- rbind(matrix(rnorm(10),,2),matrix(rnorm(10,mean=3),,2))
y <- matrix(c(rep(1,5),rep(-1,5)))

### Use as.kernelMatrix to label the cov. matrix as a kernel matrix
### which is eq. to using a linear kernel 

K <- as.kernelMatrix(crossprod(t(x)))

K

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(KERE)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/KERE/as.kernelMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: as.kernelMatrix
> ### Title: Assing kernelMatrix class to matrix objects
> ### Aliases: kernelMatrix-class as.kernelMatrix as.kernelMatrix-methods
> ###   as.kernelMatrix,matrix-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## Create toy data
> x <- rbind(matrix(rnorm(10),,2),matrix(rnorm(10,mean=3),,2))
> y <- matrix(c(rep(1,5),rep(-1,5)))
> 
> ### Use as.kernelMatrix to label the cov. matrix as a kernel matrix
> ### which is eq. to using a linear kernel 
> 
> K <- as.kernelMatrix(crossprod(t(x)))
> 
> K
An object of class "kernelMatrix"
             [,1]       [,2]       [,3]       [,4]       [,5]        [,6]
 [1,]  0.01878918 -0.1372150  0.1086256  0.2304520  0.1228437  0.03100398
 [2,] -0.13721503  1.0051019 -0.8339293 -1.7090449 -0.8201466 -0.37297448
 [3,]  0.10862561 -0.8339293  1.1719576  1.6813430 -0.3197225  2.14039067
 [4,]  0.23045195 -1.7090449  1.6813430  3.0504845  0.8458464  1.63864392
 [5,]  0.12284371 -0.8201466 -0.3197225  0.8458464  2.7531576 -3.51045812
 [6,]  0.03100398 -0.3729745  2.1403907  1.6386439 -3.5104581  7.12169126
 [7,]  0.10091773 -0.9678954  3.6733079  3.2203959 -5.1904482 11.30645429
 [8,] -0.02716205 -0.1569397  4.5974352  2.7175701 -9.1795106 17.09647179
 [9,]  0.02210567 -0.3700723  2.9196864  2.0625511 -5.1415254 10.10207518
[10,]  0.15635857 -1.4735959  5.3429944  4.7660824 -7.3824375 16.26209353
            [,7]        [,8]        [,9]      [,10]
 [1,]  0.1009177 -0.02716205  0.02210567  0.1563586
 [2,] -0.9678954 -0.15693972 -0.37007232 -1.4735959
 [3,]  3.6733079  4.59743523  2.91968642  5.3429944
 [4,]  3.2203959  2.71757006  2.06255109  4.7660824
 [5,] -5.1904482 -9.17951062 -5.14152542 -7.3824375
 [6,] 11.3064543 17.09647179 10.10207518 16.2620935
 [7,] 18.0934793 26.86096201 15.97751933 26.0549452
 [8,] 26.8609620 41.59538913 24.37036181 38.5731289
 [9,] 15.9775193 24.37036181 14.35537929 22.9673522
[10,] 26.0549452 38.57312893 22.96735217 37.5262848
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>